The Story of Two
by ReiLink
Summary: What if Shinji wished for a world that wasn't devasted by angels and all his friends lived there but they were alive. This story will take place after the End of Evangelion and it depicts the romance between Shinji and Rei who inhabit this new world they now live in. Lemon chapter guaranteed.
1. Chapter 1 - The End is the Beginning

**Chapter 1 - The End is the Beginning**

"What do you wish for?" These were the words spoken out by Rei to Shinji in the midst of the human instrumentality. She suggestively laid on top of him while they were both floating in a pool of LCL. It was weird but him having to choose what will happen to humanity by this one question was even weirder.

Every choice he made up until here now only made him suffer worse. How could Shinji himself know what he'd wish for.

"I..." He couldn't find the words to make his wish.

 _Just one slip up and we're all doomed again._ Those were the thoughts that were repeating inside his head. _What if I make a mistake again. Why do I have to choose?_ His soul was at a fight with himself but he knew he had to answer now for the sake of him and everyone else he cared for.

"...I wish to see you and everyone again. My life had some downs but without my friends and comrades I don't want to live anymore. Give humanity another chance to live their individual lives without the constant fear of world destruction." Shinji said in a calm but determined voice.

"Why me?" Rei asked, while lovingly laying her hand in Shinji's face "I'm nothing but a mere replica of your mother with some angel dna spliced in. You and the others don't need me in this world."

"I need you. You're neither my mother nor an angel. You're Rei Ayanami. I want to see you smile again." Shinji wished for as he embraced this soft hand he liked so much.

Of course there was a time when Shinji couldn't bear the fact that his mother and Ayanami looked so close to eachother but at this point he had realised that whatever he feels for Ayanami he cannot change it. Without her he'd still be all alone and she's one the reasons why he wants humanity to get another chance at life. There still were things he didn't know about her and the feeling he got from spending all this time with this one girl, made his heart feel warmer.

Rei's face changed slightly. She didn't look as worried as before but Shinji still wasn't sure what she was thinking at the moment.

"You will get hurt again." Ayanami said calmly.

"That's okay." Shinji proclaimed.

"You will suffer through hardships again." Ayanami responded in that same monotone voice.

"That's okay." Shinji proclaimed again. "You can't get the good without the bad. As long as there is a way for us to be happy I can go on with my life...Thank you, Ayanami. I hope we'll see each other again."

"Me too." Rei expressed with a slightly hurt face.

Suddenly everything around Shinji turned white. Ayanami wasn't there anymore and he asked himself if his wish did become true.

Would the world now reset? Would everyone know who he is? Would he get the chance to see Ayanami, Asuka, Misato and his friends again? What if Rei lied to him? What if he was the only one that came to this world. All alone. Forever. These were all questions Shinji asked himself.

"I don't want to be alone anymore. I don't want to be alone anymore. I don't want to be alone anymore. I don't want to be alone anymore. I don't want to be alone anymore." He repeated while waiting for something to happen.

"AYANAMI!" Shinji desperately screamed at the top of his lungs.

Darkness.

Author's notes: So this was the first chapter to my first fanfiction ever. Hope you guys liked it. I tried my best to stay as true to the characters as possible but you never know how true you stay until someone points it out. The romance between Shinji and Rei will be emphasized in this story and you'll get to see how they interact with each other in this new world they will inhabit. There will also be lemon. I would also like to note that English is only my second language so excuse me if I've made some horrible grammar mistakes.


	2. Chapter 2 - A New World

Chapter 2 - A new world

Shinji stood in an empty street. There was a thick fog going through the whole town and everything seemed really lifeless. Shinji wore his school outfit for some reason. A small light pierced through his eyes in the middle of the night. _Where does this light come from?_ He trembled a little and he had a cold feeling around his chest. Something felt uneasy.

"Did it work? Where am I?" asked the previous third children in a loud voice.

"AYANAMI, WHERE ARE YOU?!" Shinji couldn't get the feeling out of his head that something went terribly wrong. Why wasn't Rei with him? Didn't they just talk to each other?

"This wasn't a dream was it?" His eyes opened in shock a little when he thought of this.

He looked around and followed the ray of light. This was the only clue he had of this new world. After a few minutes Shinji found himself at a river and what he had found there, he couldn't believe.

"What the hell is this?" A gigantic, glowing creature appeared in front of Shinji. It had pitch black eyes and a dark core in its chest. Everything in its body appeared to be white in a glowing light. This beast also kinda looked like an Eva the more Shinji thought about it but this couldn't possibly be. Fear was going through his mind but his legs wouldn't move. He couldn't run. What would this creature do to him?

"Angels...no?" Shinji collapsed under this pressure as he felt like he couldn't take more it. His eyes were dead. _Why is this happening. Ayanami where are you. Someone please help me._ The glowing creature looked directly at Shinji and touched his head with its human-like fingers. A sudden pain flowed through young Ikari's body. Every fiber of his body felt like it was burning. This strong pain lasted for at least 5 minutes until Shinji screamed.

"AAAAAAAAAAARGH! HELP! MOM! DAD! ANYONE! HELP!"

Darkness again.

This time Shinji woke up in a hospital. He laid in a white bed with one window to his far left and the whole room painted in white. This sitiuation seemed familiar to young Ikari.

"I remember. Why do I remember? Was it this thing?"

Shinji's whole past life in this new world flowed through his head. He remembered that his father left him and his mother died when he was little but then there was another memory where his mom and dad both lived with him in a small house where they would eat and laugh together. It seemed like his new memories were the key to this new world. He knew exactly where to go now and angels never seem to existed in this alternate reality.

Some things were still unclear though. Many of the memories he had recieved only contained his parents but his friends were nowhere to be found in this whole cluster of new information. Maybe he needed time to process because it was too much for him. This was the only thing he could come up with but this didn't matter now.

"Why am I here?" said Shinji while looking at his hand confused.

If Angels didn't exist how come he ended up in a hospital? So many questions had built up in young Ikari's mind but he had to wait for someone to come in and explain this whole situation. He pressed a button for a nurse to come and indeed, an actual human being appeared infront of him.

"A-Asuka? What are you doing here?"

"Yeah. Sorry, sorry. I had to take care of another patient but I'm here now. How did you know my name?" Delievered the red haired beauty with an annoyed voice.

She wore a white shirt and short skirt. _But she's only 14 years old. How could she work at this place._ Asuka seemed more adult but how could this be? _Wait didn't she ask me something about her name?_

"Wh-What?" Shinji had to come up with something fast.

Apparently Asuke didn't remember him at all and they've never met in this world. He closely inspected her uniform to maybe find some ID-Card and there it was.

"Eeeh hehe I saw it on your ID-Card." he nervously said

"...Pervert." she said in a grimm mood.

"What? N-no I didn't mean it like this!" reponded Shinji while becoming pretty nervous.

The last time he interacted with her was after he masturbated to her comatose body so he felt like the worst human being. At one hand he was glad that she didn't remember this situation, he wasn't even sure if she knew about it, but on the other hand, he would have liked to apologize. _There is no way in hell that she would forgive me but still._ Shinji now had to live with the fact that he would never get a chance to apologize to her.

"S-So...What happened? When can I go home?"

"I could ask you the same. People found your unconcious at a river a week before. Your parents were here, vistited you and already took care of everything but they had to leave the hospital for some reason. They said that you should call them when you wake up." explained Asuka quietly.

"Thanks. So Asuka, since when have you been working here?" Shinji was confused as to why he had been in a sleep for 1 week but he needed to know more about the Asuka of this world.

"Why do you care, idiot? Do you have a thing for nurses or what? Pervert." said Asuka.

"No, but you remind me of someone I knew a while ago...Would you like to go drink some coffee sometime? Maybe we could get to know each other better." Shinji said in a quite voice.

He wasn't sure why he asked her that. Even though he knew Asuka in his previous world, he never really liked this girl. Never did she act nice to him and most of the time they just argued with each other.

"Nah kiddo. I only got this job recently and I don't want to hang out with some whiny loser patient. I have better things to do." Asuka responded

"Fine, but at least write down my number if you'll change your mind." Shinji persisted while he questioned himself why she called him kiddo. Weren't they the same age?

"Argh fine but I'm gonna call you Idiot from now. You piss me off kiddo." said Asuka with a slight blush. Shinji could never guess what Asuka from his original world thought about him. He just assumed that she hated him and he was fine with that. He already had friends and a girl that he liked so he didn't need acknowlegdement from her.

After Ikari jr. left the hospital, he immediately wanted to call his parents but something stopped him. He never spoke to his mother personally.

"I have to talk to her in person."

From what Shinji could recall, his house was near the hospital and he could slowly walk there in about 20 minutes. But Shinji ran. Shinji ran as fast as he could. Never would he have imagined to see and speak to his mother in his lifetime. This is what he had always wished for since he was a small child. Noone else mattered at this moment. After all this time he could feel the love only a mother could give. Tears started building up while he was running.  
Shinji felt like screaming out of happiness but his voice couldn't keep up with his feelings.

After a few minutes of running he had finally arrived. He was a doorstep away from seeing what he had always craved for.  
While Shinji nervously grabbed his keys, he thought about what he would say to his parents.

"Calm down. Act natural. Don't break out in tears. You musn't run away."

Shinji repeated these lines multiple times to himself so he was mentally ready.  
He slowly opened the door. A soft light blended his eyes. Two people were sitting at a couch. The house looked very well decorated with many images of angels hung everywhere. At the end of the floor he saw two people sitting at a couch. He couldn't really make it out who sat there.

"Mom...Dad?"

"SHINJI YOU'RE OKAY!" A crying woman came running towards Shinji and it was his mother. The way she looked reminded him a lot of Rei. That's no wonder because Rei was a clone of Yui. But he couldn't quite tell what the difference between their bodies were. The hair, eyes and skin were quite different but his mother seemed to have a softer face.

"Why haven't you called us. We would have come to take you home!"

As Shinji's mother hugged her son in tears, Shinji suddenly remembered that his mother did not often cry. Often she had a warm personality but it never really felt like anyone or anything could harm her.

"I-I'm home." said Shinji with a smile and tears.

"Welcome home." Yui responded while still trying to hold off her tears with a small laughter.

"I'm so sorry Shinji. I would have stayed with you but your father and I had to go working. You know how many hours we have to work at the laboratory. Your dad even wanted to work for me but if he had done that then you and him would have spent your time at the hospital." said Yui.

"That's okay mom."  
There were worse things he already had to go through with his parents in the world where Shinji came from. Something like this couldn't hurt him anymore.

Silence. Both just looked at each other in happiness. Shinji wasn't sure what to say even though he tried to come up with something. It seemed like Yui also wasn't sure what to tell him. Not the way the son had expected to have a reunion with his mom after such a long time.

"...Sooo is dad also here?" Shinji asked.

"Huh? Uh no. He's at work but someone waited for you to come home." said Yui. She looked a bit confused and worried. Maybe the sudden shock of her seeing her son alive and well, was a bit too much for.

"Wait. But I didn't call you. How long did that person wait?" Shinji asked

"Well, she waited since yesterday. She also got hospitalized the same day as you did but she woke up sooner. I almost thought you two were involved in the same accident." Yui responded.

Someone suddenly appeared behind Yui.

"Ayanami."

Author's note: Yeah Rei didn't appear in this chapter, but I had to establish the world and some important characters first before I got to the meat of the story. Of course the next chapter will be entirely ShinRei centric but we also need to know more about this world. Maybe some people didn't notice but I took insperation for some little story ideas from the NGE Game: Girlfriend of steel 2. Not a great game but it had some cool ideas and concepts thrown in that I would like to expand on.  
Of course I still have no idea how long this story will take to finish but expect at least 10 chapters with this length from me.


	3. Chapter 3 - Rei I

**Chapter 3 - Rei I**

The sun started going down. The clock was ticking. Time was slowing down for Shinji. Out of all the scenarios that could have happened, how could Rei appear at a time and place like this directly after his meeting with his mom and Asuka. This world couldn't possibly be that small.  
Someone or something had to plan out these actions and meetings. Was it this gigantic, glowing creature that touched Shinji?  
What reason would it have to place all of these people together in the same city at the same time.  
Shinji's head hurt. Rei just kept staring at him and an even weirder atmosphere built around this whole room. Yui also didn't know what to think of that situation.

"Ikari-kun. I'm glad you're okay." Ayanami said.

"Aaah...Thanks. I-I'm also glad you're okay." Shinji replied.

He couldn't look at her face. Ayanami searched for him and even waited this long to check if he's okay but Shinji...The shame he felt from selfishly trying to search for his parents before confirming that Rei was okay, made him sweat nervously. Shinji knew his parents were okay but still he didn't even try to search for Rei. Maybe it was the fear of him finding that she would be dead made him search for his parents first. No. This excuse would be too convinient for him. Shinji's mother noticed that something related to Rei tormented her son.

"Shinji, maybe you two should go to your room. It seems like you have a lot to talk about. I'll have to go to work now anyway. We'll talk later when I'm back, okay? And don't do anything weird with her." Yui said with a playful smile on her face.

"What? No!" Shinji responded with an embarrased look.

Rei and Shinji were going up some stairs. The Ikari family house was relativly big on the inside. On the first floor you could go to the kitchen, the living room and and and his parents' bed room. On the the second floor you could go to an empty room, the bath and finally Shinji's room.  
Both Rei and Shinji entered young Ikari's room and sad down on his bed. It seemed like Rei wanted to sit closer to Shnji but she decided against it, at the last moment so there was a certain distance between them. They had the same look on their faces. No one seemed to really grasp what was going on so they could neither smile nor glower.

"Ikari-kun..." Rei said in a quite monotone voice.

"Ayanami...S-so how are you doing?" Shinji asked nervously.

Shnji wasn't sure if Rei could remember what happened before he ended up in this world. He wanted to go easy about it because Asuka didn't remember anything all and he was sure that no one else could also remember anything.

"I am okay and I am sorry for suddenly showing up. I was afraid that something happened to you...Do you remember what happened to you?" Rei asked but this time with a slightly worried face.

"W-What do you mean?" Shinji responded but he knew what she meant.

How could he answer this.

"This white creature..." She said.

"What? You saw it too?!" Shinji screamed out loud.

He quickly tried to silence himself with a red face.

"So do you remember the third impact? What happened? Where were you? What was that thing? Why are we ol-" Shinji asked quickly but Rei interrupted him.

"I know as much as you. The only thing I remember is that I woke after third impact and this creature touched me. After this happened, I woke up in a hospital with memories of my family and friends. This happened a year ago." Rei said.

"One year? Why didn't you try to contact me sooner? Why can't I remember you in this world..." Shinji asked with a sad smile.

He just had noticed that Ayanami were nowhere in his new memories. In his mind he knew what answer would come. _She probably rejected me. Who would she even search for a guy like me._ That's what he thought.

"In this world I'm not from Japan. I moved in here on the other side of this town 2 weeks ago and trying to find you was hard without any clues. It also seems like I am still distantly related to your mother, Ikari-kun." Rei answered.

This was a lot of information to swallow for one person. Shinji's head was spinning and if he didn't knew any better he would have branded Rei as a crazy person. At least she tried to search for him. This gave him hope that their relationship could grow a little.

"Wait. Ayanami...are you the Ayanami I know or are you the replacement of the Ayanami that died in the fight with the angel?"

Shinji didn't know how to ask Rei that question so he just flat out said what he wanted to know. He thought that he sounded rude this was too important for him to just ignore it.

"I contain memories of all 3 Ayanamis so you could say that I'm all of them but I am just me. I am not like the second me but I'm also not like the third me." She responded with a cold voice.

 _Three Ayanamis? So was there another one before I first met her?_ Shinji put his finger on his chin and tried to puzzle the pieces together. There were many things he didn't know about in his original world but at his point in time he didn't care anymore. He wanted to start a new life in this world so he gave up questioning more things about his old life in the lost world. Ayanami was Ayanami, so he didn't care as long as she lived and remembered him.

"I am just happy to see you again. I don't know what I would have done, if I never got see you again..." Shinji said to her with a smile, while he looked at her red eyes.

Rei blushed. She couldn't look at him and didn't know how to respond to his statement. Never has anyone said something like this to her. Even in this world, her parents abandoned her and she grew up in orphanage. It also didn't help that she didn't have any friends. She wasn't bullied or anything but everyone ignored her and she spent her time alone thinking about anything that came across her mind. Back when she was in school, the only friends she had were her books and her life was meaningless. Books were the only thing that could distract her from her misery. Gendo wasn't there to give her a purpose in life and the old Ayanami in this world was suicidal.

Since Rei arrived here in this world, 1 year had passed and she felt how all of her personalities mixed up together and this even contained the Rei of this world. Not only did she get those memories but she had a feeling, how she didn't want to live anymore. Ayanami had nothing and there was no clue of Shinji. Rei considered suicide to just end it but she remembered the third impact. She remembered that Shinji said that she wanted to see her again so she clung on to that hope.

Rei's heart skipped a few bits. The only thing in her mind was Shinji and now that she sat alongside him again, after all this time made her mind go blank.

"Would you mind if we get to see each other from time to time?" Rei asked while she looked to the ground. Her voice still sounded cold and monotone.

"S-sure, if you don't mind talking with someone like me...I wouldn't mind seeing you everyday if that's okay with you. After all I wanted the chance to talk to you again after third impact." Shinji answered

He couldn't look at Rei's face anymore. This was too embarrassing of an answer. A few minutes past of them saying nothing too each other. Just silence. It wasn't the awkward kind of silence though. Something felt strangely confortable about it. Both Shinji and Rei suddenly started smiling a little bit.

"You know Ayanami. Can you tell me more about you in this world. What were you doing before you got here? I want to know everything!" Shinji abrubtly asked Rei.

Rei feared that this question would come. Her old self wouldn't have felt any embarrassment over a question like this, but since she had changed, Rei panicked a lot.  
Of course Shinji couldn't notice because she was good of hiding her pain after years all the years in her old world.

They talked through the whole night. Rei explained how she never had anyone in this lifetime and the only thing she had was the hope to see Shinji again. Shinji on the other hand told her about how great his life had been. He had a lot of friends and even Toji and the other guys were in contact with him. Every little detail was told in this night and it seemed like now they knew everything about each other. Both of them were 19 years old and they had finished school. The sun started to rise.

"At this point in time I'm not working. It seems like I finished school but I'm still living at my parents' home. I don't have any idea what I'm going to do now. What about you?" Shinji said.

"I'm working as a librarian. It's quite and I don't earn that much, but it is a good distraction for myself." No emotion was shown and it looked like Rei was tired.

Shinji was depressed. Now that he knew what Rei has been going through, he just wanted to help her in any way shape or form. The young Ikari didn't want her to just cling to him until she died. She was better than this. She deserved better. Shinji didn't want to become like his old father that used Rei's blind commitment to use her for whatever he needed.  
There had to be a way to help her. He grabbed her left hand and looked directly at her.

"Ayanami." Shinji said with a confident voice and face.

"Yes?" Rei asked.

"Would you like to move into our house?" He still had the same look but this time, he blushed a little.

Rei kept staring at Shinji. No emotion was shown by her. She didn't know what to say to him right know. A request like this one came out of the sudden and she didn't know what his exact intention was.

"S-sure but are your parents fine with this?" Rei asked in a quite voice.

"We have a free room left and you're part of the family, kinda, so I'm sure she won't have anything against this." Shinji answered with a confident smile.

He wasn't really sure if his parents would allow a request like this but he couldn't leave Ayanami like this so he had to try and do it. He had his own demons to fight with but Rei was the only one that could understand him and maybe both of them together could live on to fight this pain, they had to go through in their previous lives. This was something he wished for.

"Thank you, Ikari-kun." Rei responded to Shinji with a warm smile on her face.

Author's note: Lots of expostion in this chapter but I tried to make the dialogue sound natural for the characters. Now that we got the exposition out of the way, I will try to solely focus on the relationship of Shinji and Rei. Asuka, Yui and Kaworu will maybe get bigger roles but I haven't decided on this yet. I'm also not sure what kind of ending I want to make. Maybe it will end in tragedy. Maybe not. This is Evangelion after all and anything is possible in this series. Hope that you liked this chapter and if you thought that somehow the characters acted ooc, be sure to let me know.


End file.
